Article
Biochemical Research Methods
Christoffer Edlund, Timothy R. Jackson, Nabeel Khalid, Nicola Bevan, Timothy Dale, Andreas Dengel, Sheraz Ahmed, Johan Trygg, Rickard Sjoegren
Summary: The LIVECell dataset consists of annotated phase-contrast images of over 1.6 million cells, aiming to improve the training of image segmentation models through deep learning. Its creation and utilization help explore biological phenomena and conduct high-throughput quantitative imaging studies.
Review
Biochemistry & Molecular Biology
Herbert Schneckenburger
Summary: Laser plays an increasing role in live cell microscopy due to its unique properties. It is used in various techniques such as 3D microscopy, super-resolution microscopy, spectral imaging, and fluorescence lifetime imaging. Laser applications in live cell biology include fluorescence diagnosis, photodynamic therapy, and laser-assisted optoporation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Jeremy Copperman, Sean M. Gross, Young Hwan Chang, Laura M. Heiser, Daniel M. Zuckerman
Summary: Time-lapse imaging is a powerful tool to study cell dynamics, but analyzing morphological changes over time is challenging. In this study, we use trajectory embedding to analyze cellular behavior based on multiple time points simultaneously. We apply this method to study the effects of microenvironmental perturbagens on MCF10A mammary epithelial cells. Our analysis reveals ligand-specific regulation of cell state transitions and provides descriptive models of single-cell trajectories. Incorporating trajectories improves the characterization of cell states and enables better identification of phenotypes compared to snapshot-based analysis. This approach has broad applications in live-cell imaging for studying cell responses.
COMMUNICATIONS BIOLOGY
(2023)
Article
Optics
Zewei Luo, Ge Wu, Mengting Kong, Zhi Chen, Zhengfei Zhuang, Junchao Fan, Tongsheng Chen
Summary: Forster resonance energy transfer (FRET) microscopy is a valuable tool for studying biological systems, but super-resolution FRET imaging in living cells is challenging. In this study, we propose a SR FRET method called SIM-FRET that combines SR structured illumination microscopy (SIM) imaging and acceptor sensitized emission FRET imaging to achieve live-cell quantitative SR FRET imaging. Our method provides enhanced spatial resolution and maintains the advantages of quantitative FRET analysis. We validate the effectiveness of SIM-FRET through simulated models and live-cell samples, and demonstrate its ability to reveal the intricate structure of FRET signals.
PHOTONICS RESEARCH
(2023)
Article
Cell Biology
Joanna W. Pylvanainen, Estibaliz Gomez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Summary: Live imaging, particularly when combined with fluorescence microscopy, is a powerful tool for observing cellular components in real time. However, implementing live imaging and analyzing the resulting datasets is challenging due to issues such as drift, phototoxicity, and dataset size. Recent advances in bioimage analysis, including deep learning, are revolutionizing how live imaging is performed. Important computational methods for live imaging include drift correction, denoising, super-resolution imaging, artificial labeling, tracking, and time series analysis. Self-driving microscopy has also seen recent advancements.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Yang Zhang, Yeting Zheng, Andrea Tomassini, Ambarish Kumar Singh, Francisco M. Raymo
Summary: PALM uses fluorescence photoactivation and single-molecule localization to overcome optical diffraction and achieve nanoscale spatial resolution in imaging biological samples. Synthetic modifications of the BODIPY chromophore allow for photoactivation and precise localization of single molecules. In combination with targeting ligands, photoactivatable BODIPYs can label subcellular components and enable sub-diffraction imaging of live cells using PALM, making them valuable probes for bioimaging applications.
Article
Biotechnology & Applied Microbiology
Andreas Boden, Francesca Pennacchietti, Giovanna Coceano, Martina Damenti, Michael Ratz, Ilaria Testa
Summary: A new 3D pRESOLFT microscope method with sub-80-nm resolution has been developed to visualize the volumetric architecture of organelles and molecules inside whole living cells, allowing for targeted 3D confinement of fluorescence and observation of dynamic structural alterations in cells.
NATURE BIOTECHNOLOGY
(2021)
Review
Optics
Herbert Schneckenburger, Verena Richter
Summary: This short overview discusses 3D live cell imaging, relevant samples, challenges like optical sectioning and phototoxicity, and enhanced microscopy methods with some examples and applications. Future advancements may involve increasing microscopic resolution and utilizing molecular sensing techniques.
Article
Biochemistry & Molecular Biology
Anayat Bhat, Shuang Li, Daniel Hammler, Martin J. Winterhalder, Andreas Marx, Andreas Zumbusch
Summary: The hydrolysis of nucleotides is important for cellular energy, and the transfer of phosphates to proteins is crucial for post-translational modification. A novel fluorogenic adenosine 5'-tetraphosphate (Ap4) analog has been developed for real-time monitoring of ATP hydrolysis within live cells, with potential applications in studying cellular processes involving Ap4 hydrolysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Weisong Zhao, Shiqun Zhao, Liuju Li, Xiaoshuai Huang, Shijia Xing, Yulin Zhang, Guohua Qiu, Zhenqian Han, Yingxu Shang, De-En Sun, Chunyan Shan, Runlong Wu, Lusheng Gu, Shuwen Zhang, Riwang Chen, Jian Xiao, Yanquan Mo, Jianyong Wang, Wei Ji, Xing Chen, Baoquan Ding, Yanmei Liu, Heng Mao, Bao-Liang Song, Jiubin Tan, Jian Liu, Haoyu Li, Liangyi Chen
Summary: Sparse structured illumination microscopy (Sparse-SIM) achieves nearly twofold resolution enhancement by utilizing sparse deconvolution algorithm, enabling the resolution of intricate biological structures such as small fusion pores, nuclear pores, and relative movements of inner and outer mitochondrial membranes.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Rajesh Ranjan, Xin Chen
Summary: This study presents a method for conducting super-resolution timelapse fluorescence live cell imaging in situ, compatible with low fluorescent intensity cells and capable of visualizing multiple subcellular structures. Special procedures in sample preparation and immobilizing specimens are necessary for this technique, but it is broadly applicable to various cell types.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Michelle S. Frei, Birgit Koch, Julien Hiblot, Kai Johnsson
Summary: Fluorescence lifetime multiplexing using fluorescent probes with distinct lifetimes but similar spectral properties enables multi-channel imaging in living cells. Among 18 synthetic probes, we identified 8 pairwise combinations suitable for multiplex imaging. Combining self-labeling protein tags, we can image up to 8 different biological targets, effectively increasing the number of observable targets. The combination of synthetic probes and fluorescence lifetime multiplexing is a powerful live-cell imaging technique.
ACS CHEMICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Alice Sandmeyer, Lili Wang, Wolfgang Huebner, Marcel Mueller, Benjamin K. Chen, Thomas Huser
Summary: Cost-effective, highly portable, and easy to use high-resolution live-cell imaging systems can revolutionize research in challenging environments, enabling real-time tracking of virus particles and studying infection mechanisms.
Article
Chemistry, Analytical
Qian Wang, Hua He, Qian Zhang, Zhenzhen Feng, Jiqiang Li, Xiaoliang Chen, Lihua Liu, Xiaojuan Wang, Baosheng Ge, Daoyong Yu, Hao Ren, Fang Huang
Summary: The developed deep-learning assisted single-molecule imaging method can accurately distinguish between monomers and complexes, allowing for real-time tracking of protein interactions with a high accuracy rate.
ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Zrinko Baricevic, Zahra Ayar, Samuel M. Leitao, Miranda Mladinic, Georg E. Fantner, Jelena Ban
Summary: Time-lapse light microscopy combined with in vitro neuronal cultures has made a significant contribution to Developmental Neuroscience. Although fluorescently labeled tags and dyes have provided advancements in cell imaging, long-term recordings remain challenging due to phototoxicity and interference with cell physiology. Hence, label-free high-resolution methods, such as scanning ion conductance microscopy (SICM) or digital holography microscopy (DHM) are proposed for studying live cell dynamics during neuronal development and regeneration.
Editorial Material
Plant Sciences
Mohd Fadhli Hamdan, Goetz Hensel, Anshu Alok, Boon Chin Tan
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Leo Bellin, Michael Melzer, Alexander Hilo, Diana Laura Garza Amaya, Isabel Keller, Joerg Meurer, Torsten Moehlmann
Summary: Nucleotide limitation and imbalance in plants have important consequences on metabolism and gene expression. In this study, we investigated the role of two organellar localized enzymes, chloroplast aspartate transcarbamoylase (ATC) and mitochondrial dihydroorotate dehydrogenase (DHODH), in pyrimidine metabolism. Knock-down mutants of ATC showed severe phenotypic effects, including low pyrimidine nucleotide levels, reduced photosynthetic capacity, and altered leaf morphology. DHODH knock-down mutants exhibited impaired seed germination and altered mitochondrial ultrastructure. Our findings suggest that ATC and DHODH play critical roles in nucleotide metabolism and have far-reaching effects on plant growth and development.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Volodymyr Radchuk, Zeinu M. Belew, Andre Guendel, Simon Mayer, Alexander Hilo, Goetz Hensel, Rajiv Sharma, Kerstin Neumann, Stefan Ortleb, Steffen Wagner, Aleksandra Muszynska, Christoph Crocoll, Deyang Xu, Iris Hoffie, Jochen Kumlehn, Joerg Fuchs, Fritz F. Peleke, Jedrzej J. Szymanski, Hardy Rolletschek, Hussam H. Nour-Eldin, Ljudmilla Borisjuk
Summary: This study focuses on the functionality of the SWEET family of barley and reveals the crucial role of HvSWEET11b in the distribution of sugars and cytokinins during grain development. Knocking down HvSWEET11b leads to impaired grain development, disrupted sugar and cytokinin distribution, and changes in grain size, starch content, and protein content. The findings highlight the important regulatory role of HvSWEET11b in barley grain filling.
Review
Plant Sciences
Teodoro Cardi, Jana Murovec, Allah Bakhsh, Justyna Boniecka, Tobias Bruegmann, Simon E. Bull, Tom Eeckhaut, Matthias Fladung, Vladislava Galovic, Anna Linkiewicz, Tjasa Lukan, Isabel Mafra, Krzysztof Michalski, Musa Kavas, Alessandro Nicolia, Justyna Nowakowska, Laszlo Sagi, Cecilia Sarmiento, Kubilay Yildrim, Milica Zlatkovic, Goetz Hensel, Katrijn Van Laere
Summary: The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. It has been widely used for plant research and breeding, but many challenges and bottlenecks still hinder its further improvement and application.
TRENDS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Suriya Tamilselvan-Nattar-Amutha, Stefan Hiekel, Franziska Hartmann, Jana Lorenz, Riddhi Vijay Dabhi, Steven Dreissig, Goetz Hensel, Jochen Kumlehn, Stefan Heckmann
Summary: Genome editing in barley usually involves Agrobacterium-mediated transformation and tissue culture techniques, which are genotype-dependent and time-consuming. Recently, a virus-induced genome editing method using barley stripe mosaic virus (BSMV) was developed. This method enables rapid somatic and heritable gene editing in Cas9-transgenic barley. The study showed successful editing in the ALBOSTRIANS gene and meiosis-related candidate genes in barley.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Yongyu Huang, Roop Kamal, Nandhakumar Shanmugaraj, Twan Rutten, Venkatasubbu Thirulogachandar, Shuangshuang Zhao, Iris Hoffie, Goetz Hensel, Jeyaraman Rajaraman, Yudelsy Antonia Tandron Moya, Mohammad-Reza Hajirezaei, Axel Himmelbach, Naser Poursarebani, Udda Lundqvist, Jochen Kumlehn, Nils Stein, Nicolaus von Wiren, Martin Mascher, Michael Melzer, Thorsten Schnurbusch
Summary: Flowering plants with indeterminate inflorescences often produce more floral structures than necessary. In barley (Hordeum vulgare L.), the initiation and maturation of floral primordia are molecularly decoupled. Initiation is primarily controlled by flowering-time genes, while floral growth is regulated by barley CCT MOTIF FAMILY 4 (HvCMF4) through light signaling, chloroplast, and vascular developmental programs. Mutations in HvCMF4 result in increased primordia death and pollination failure due to reduced rachis greening and limited energy supply to floral tissues. HvCMF4 is proposed to be a light sensory factor that coordinates floral initiation and survival with the vascular-localized circadian clock. Notably, stacking beneficial alleles for primordia number and survival has positive implications for grain production. These findings offer insights into the molecular mechanisms of grain number determination in cereal crops.
Article
Plant Sciences
Christian Hertig, Twan Rutten, Michael Melzer, Jos H. M. Schippers, Johannes Thiel
Summary: Endosperm development in barley involves the formation of a multinucleate syncytium and subsequent cellularization, leading to the differentiation of endosperm transfer cells (ETCs) and aleurone cells (AL). The positional signaling in the syncytial stage determines the cell identity in the cereal endosperm. This study used morphological analysis and RNA-seq to investigate the developmental and regulatory programs directing cell specification in early endosperm. The results revealed specific characteristics and identified signaling pathways and transcription factors involved in ETC and AL specification.
Article
Plant Sciences
Agata Daszkowska-Golec, Devang Mehta, R. Glen Uhrig, Agnieszka Braszewska, Ondrej Novak, Irene M. Fontana, Michael Melzer, Tomasz Plociniczak, Marek Marzec
Summary: We used a combination of transcriptomics, proteomics, and phytohormonomics analyses to investigate the SL-dependent mechanisms associated with water deficit response in barley. Our research revealed the role of SLs in alleviating the effects of water limitation on plants and identified potential strategies for developing drought-resistant barley.
Letter
Plant Sciences
Mariana Demarchi, Rocio C. Arce, Mabel Campi, Juan J. Pierella Karlusich, Mohammad-Reza Hajirezaei, Michael Melzer, Anabella F. Lodeyro, Raquel L. Chan, Nestor Carrillo
Article
Plant Sciences
Aleksandra Chojnacka, Aleksandra Smoczynska, Dawid Bielewicz, Andrzej Pacak, Goetz Hensel, Jochen Kumlehn, Maciej Karlowski Wojciech, Magda Grabsztunowicz, Ewa Sobieszczuk-Nowicka, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Summary: This study finds that microRNA444 from the MIR444 gene family is involved in regulating the expression of transcription factors in barley. The study also shows that these genes undergo alternative splicing to produce functional and nonfunctional transcripts. Additionally, experimental evidence suggests that PEP444c is involved in the biogenesis of microRNA444c in barley.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Plant Sciences
Gerit Bethke, Yadong Huang, Goetz Hensel, Shane Heinen, Chaochih Liu, Skylar R. Wyant, Xin Li, Maureen B. Quin, Susan Mccormick, Peter L. Morrell, Yanhong Dong, Jochen Kumlehn, Silvio Salvi, Franz Berthiller, Gary J. Muehlbauer
Summary: Through studying 496 barley accessions, it was found that the UGT13248 gene plays a role in resistance to Fusarium head blight (FHB) by converting DON to D3G, a nontoxic form; two mutant alleles (T368I and H369Y) were identified that increase FHB severity and reduce D3G production.
Article
Plant Sciences
Gesa Helmsorig, Agatha Walla, Thea Ruetjes, Gabriele Buchmann, Rebekka Schueller, Goetz Hensel, Maria von Korff
Summary: The eam7 locus in barley controls photoperiodic flowering by modifying the diurnal expression pattern of the major photoperiod response gene Ppd-H1.
Review
Biotechnology & Applied Microbiology
Sunny Ahmar, Goetz Hensel, Damian Gruszka
Summary: Cereal crops play a significant role in human consumption and animal feed, but face challenges from climate change and population expansion. Gene-editing technologies, such as CRISPR/Cas9, offer a potential solution to develop stress-tolerant and high-yielding cereal varieties. However, there are challenges to overcome, including time-consuming processes, limited genotypes for transformation, and restrictive regulations on genetically modified organisms (GMOs).
BIOTECHNOLOGY ADVANCES
(2023)
Article
Biochemistry & Molecular Biology
Indira Saado, Khong-Sam Chia, Ruben Betz, Andre Alcantara, Aladar Pettko-Szandtner, Fernando Navarrete, John C. D'Auria, Michael Kolomiets, Michael Melzer, Ivo Feussner, Armin Djamei
Summary: The study shows that the smut fungus Ustilago maydis secretes effector proteins to suppress host defense responses in maize plants, with Rip1 playing a key role in inhibiting host immunity and affecting antioxidant reactions. By relocalizing the host factor ZmLox3, the fungus can partially suppress ROS burst responses in maize plants.
